How to close an open manifold?
You could select the edges on the border using AltRMB  in Edit Mode. Press space to show the popup menu and type Grid Fill.



If you want the filled area flat you can scale the z-axis SZ0. 



In order to edit a high poly mesh in Blender created by sculpting or importing 3D-scans usually retopology is required.

Related:


How should I handle a split in a retopology?
Is there a way to &quot;rescue&quot; mesh that has very bad topology?